Fig. 3
From: Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data
Validation of predicted targets of the USF2-NFYA complex using ChIP-qPCR and RT-PCR. a ChIP-qPCR with a NFYA pull-down and qPCR amplification against CST NFYA-USF2-predicted target genes. The genomic DNA from K562 cells (left panel) and HeLa cells (right panel) that immunoprecipitated with NFYA and nonspecific IgG antibodies was used for qPCR to assess the fold enrichment of the respective gene promoters in NFYA-IP DNA over IgG-IP for each gene. The fold enrichments were the averages of three independent experiments and the data were presented as the means ± standard errors. HoxB4 was used as a positive control (see Methods). b Same as (a) with a USF2 pull-down. c The expression level of USF2 in HeLa cells with USF2 silencing by siRNA. Upper panel: Western blot; β-tubulin: internal control. Lower panel: real-time RT-PCR; TBP: internal control. d The expression levels of three downstream genes of USF2 in HeLa cells with USF2 silencing, as determined by real-time RT-PCR. *P < 0.05, compared with scramble control